Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this
to extract flanking regions for cloning. If the result of the multiple sequence alignment is
not as expected, these results could be used for further investigation.
qseqid
sseqid
percentage.identical
alignment.length
no.mismatch
no.gap.openings
qstart
qend
sstart
send
evalue
bitscore
0
TraesCS2D01G054400
chr2D
100.000
2690
0
0
1
2690
21742123
21744812
0.000000e+00
4968.0
1
TraesCS2D01G054400
chr2D
98.699
2691
30
3
1
2690
21769857
21772543
0.000000e+00
4771.0
2
TraesCS2D01G054400
chr2D
89.552
1943
115
44
654
2546
21617082
21618986
0.000000e+00
2383.0
3
TraesCS2D01G054400
chr2D
94.189
1566
62
17
880
2435
21639672
21641218
0.000000e+00
2361.0
4
TraesCS2D01G054400
chr2D
94.258
1463
63
13
953
2414
21662152
21663594
0.000000e+00
2217.0
5
TraesCS2D01G054400
chr2D
94.258
1463
63
13
953
2414
21678567
21680009
0.000000e+00
2217.0
6
TraesCS2D01G054400
chr2D
95.469
309
12
2
261
568
21659675
21659982
2.410000e-135
492.0
7
TraesCS2D01G054400
chr2D
95.146
309
13
2
261
568
21676079
21676386
1.120000e-133
486.0
8
TraesCS2D01G054400
chr2D
94.822
309
14
2
261
568
21633693
21634000
5.210000e-132
481.0
9
TraesCS2D01G054400
chr2D
93.403
288
18
1
632
918
21661861
21662148
2.480000e-115
425.0
10
TraesCS2D01G054400
chr2D
93.403
288
18
1
632
918
21678276
21678563
2.480000e-115
425.0
11
TraesCS2D01G054400
chr2D
91.005
189
17
0
632
820
21635866
21636054
3.440000e-64
255.0
12
TraesCS2D01G054400
chr2D
97.222
144
4
0
2547
2690
164771481
164771624
7.440000e-61
244.0
13
TraesCS2D01G054400
chr2D
95.918
147
6
0
2544
2690
300509007
300508861
3.460000e-59
239.0
14
TraesCS2D01G054400
chr2D
94.366
142
4
1
2412
2549
21663629
21663770
5.830000e-52
215.0
15
TraesCS2D01G054400
chr2D
94.366
142
4
1
2412
2549
21680044
21680185
5.830000e-52
215.0
16
TraesCS2D01G054400
chr2D
92.254
142
7
1
2412
2549
21641230
21641371
5.870000e-47
198.0
17
TraesCS2D01G054400
chr2D
82.648
219
33
4
43
258
103149234
103149018
3.540000e-44
189.0
18
TraesCS2D01G054400
chr2D
92.857
70
5
0
569
638
21635744
21635813
4.740000e-18
102.0
19
TraesCS2D01G054400
chr2A
90.638
1709
117
21
632
2331
23864010
23865684
0.000000e+00
2230.0
20
TraesCS2D01G054400
chr2A
94.927
887
42
1
986
1869
23826122
23827008
0.000000e+00
1386.0
21
TraesCS2D01G054400
chr2A
86.071
481
35
13
2095
2546
23827128
23827605
3.110000e-134
488.0
22
TraesCS2D01G054400
chr2A
90.415
313
21
5
632
938
23825509
23825818
1.160000e-108
403.0
23
TraesCS2D01G054400
chr2A
88.704
301
18
7
339
635
23825089
23825377
1.180000e-93
353.0
24
TraesCS2D01G054400
chr2A
88.276
290
18
6
2273
2547
23865679
23865967
1.540000e-87
333.0
25
TraesCS2D01G054400
chr2B
95.479
1305
53
5
891
2195
34867204
34865906
0.000000e+00
2078.0
26
TraesCS2D01G054400
chr2B
91.781
1387
75
13
1169
2549
34954092
34952739
0.000000e+00
1893.0
27
TraesCS2D01G054400
chr2B
94.681
376
18
2
264
638
35012294
35011920
1.390000e-162
582.0
28
TraesCS2D01G054400
chr2B
89.971
339
20
5
2225
2549
34865909
34865571
2.480000e-115
425.0
29
TraesCS2D01G054400
chr2B
92.670
191
13
1
632
821
35011888
35011698
9.490000e-70
274.0
30
TraesCS2D01G054400
chr2B
89.202
213
18
4
650
860
34867411
34867202
7.390000e-66
261.0
31
TraesCS2D01G054400
chr2B
81.517
211
34
5
1
208
368313517
368313309
4.610000e-38
169.0
32
TraesCS2D01G054400
chrUn
100.000
408
0
0
694
1101
477929041
477928634
0.000000e+00
754.0
33
TraesCS2D01G054400
chr5D
97.203
143
4
0
2548
2690
397380580
397380438
2.680000e-60
243.0
34
TraesCS2D01G054400
chr5D
97.203
143
4
0
2548
2690
536762330
536762472
2.680000e-60
243.0
35
TraesCS2D01G054400
chr5D
96.552
145
5
0
2546
2690
169481590
169481734
9.620000e-60
241.0
36
TraesCS2D01G054400
chr5D
95.333
150
6
1
2541
2690
500156420
500156568
1.240000e-58
237.0
37
TraesCS2D01G054400
chr7D
95.918
147
6
0
2544
2690
220500787
220500933
3.460000e-59
239.0
38
TraesCS2D01G054400
chr7D
82.648
219
33
4
43
258
601942070
601942286
3.540000e-44
189.0
39
TraesCS2D01G054400
chr7D
80.288
208
35
5
43
247
563541389
563541185
4.640000e-33
152.0
40
TraesCS2D01G054400
chr7D
76.587
252
50
7
19
265
555544648
555544895
2.170000e-26
130.0
41
TraesCS2D01G054400
chr5B
95.918
147
5
1
2544
2690
178555411
178555266
1.240000e-58
237.0
42
TraesCS2D01G054400
chr5B
89.583
144
10
5
108
248
521853018
521852877
7.650000e-41
178.0
43
TraesCS2D01G054400
chr6D
77.135
363
54
14
1988
2339
457592195
457591851
1.640000e-42
183.0
44
TraesCS2D01G054400
chr4D
90.071
141
9
5
108
245
509045655
509045517
7.650000e-41
178.0
45
TraesCS2D01G054400
chr1B
81.517
211
34
5
1
208
180693682
180693890
4.610000e-38
169.0
46
TraesCS2D01G054400
chr5A
89.286
56
5
1
16
70
622375929
622375874
4.810000e-08
69.4
These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the
BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are
purely upstream or downstream may be removed if they don't overlap both primers.
query
scaffold
start
end
length
rev.comp
avg.bitscore
max.bitscore
avg.percent.identical
query.start
query.end
num_hsp
groupid
homo_length
0
TraesCS2D01G054400
chr2D
21742123
21744812
2689
False
4968.000000
4968
100.000000
1
2690
1
chr2D.!!$F2
2689
1
TraesCS2D01G054400
chr2D
21769857
21772543
2686
False
4771.000000
4771
98.699000
1
2690
1
chr2D.!!$F3
2689
2
TraesCS2D01G054400
chr2D
21617082
21618986
1904
False
2383.000000
2383
89.552000
654
2546
1
chr2D.!!$F1
1892
3
TraesCS2D01G054400
chr2D
21659675
21663770
4095
False
837.250000
2217
94.374000
261
2549
4
chr2D.!!$F6
2288
4
TraesCS2D01G054400
chr2D
21676079
21680185
4106
False
835.750000
2217
94.293250
261
2549
4
chr2D.!!$F7
2288
5
TraesCS2D01G054400
chr2D
21633693
21641371
7678
False
679.400000
2361
93.025400
261
2549
5
chr2D.!!$F5
2288
6
TraesCS2D01G054400
chr2A
23864010
23865967
1957
False
1281.500000
2230
89.457000
632
2547
2
chr2A.!!$F2
1915
7
TraesCS2D01G054400
chr2A
23825089
23827605
2516
False
657.500000
1386
90.029250
339
2546
4
chr2A.!!$F1
2207
8
TraesCS2D01G054400
chr2B
34952739
34954092
1353
True
1893.000000
1893
91.781000
1169
2549
1
chr2B.!!$R1
1380
9
TraesCS2D01G054400
chr2B
34865571
34867411
1840
True
921.333333
2078
91.550667
650
2549
3
chr2B.!!$R3
1899
10
TraesCS2D01G054400
chr2B
35011698
35012294
596
True
428.000000
582
93.675500
264
821
2
chr2B.!!$R4
557
AutoCloner calculated primer pairs
These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3),
whilst remaining within the specified product range where possible.
Listed here are all possible primers based on the multiple sequence alignment and SNPs generated
previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work
during PCR or sequencing,
these could be used as alternatives.